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Denoise MNI152NLin6Asym:res-2 #40

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merged 3 commits into from
Aug 6, 2024
Merged

Denoise MNI152NLin6Asym:res-2 #40

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f4fec1f
Denoise MNI152NLin6Asym:res-2 data.
tsalo Aug 6, 2024
b2d88c2
Update base.py
tsalo Aug 6, 2024
0a2674a
Update aroma.py
tsalo Aug 6, 2024
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8 changes: 5 additions & 3 deletions src/fmripost_aroma/workflows/aroma.py
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Original file line number Diff line number Diff line change
Expand Up @@ -471,7 +471,7 @@
(inputnode, ds_denoised, [
('space', 'space'),
('cohort', 'cohort'),
('resolution', 'res'),
('resolution', 'resolution'),
]),
(add_non_steady_state, ds_denoised, [('bold_add', 'in_file')]),
]) # fmt:skip
Expand All @@ -497,7 +497,7 @@
if skip_vols == 0:
return bold_file

out = fname_presuffix(bold_file, suffix='_cut', newpath=os.getcwd())
out = fname_presuffix(bold_file, prefix='cut_', newpath=os.getcwd())

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src/fmripost_aroma/workflows/aroma.py#L500 

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bold_img = nb.load(bold_file)
bold_img.__class__(
bold_img.dataobj[..., skip_vols:], bold_img.affine, bold_img.header
Expand All @@ -507,6 +507,8 @@

def _add_volumes(bold_file, bold_cut_file, skip_vols):
"""Prepend skip_vols from bold_file onto bold_cut_file."""
import os

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import nibabel as nb
import numpy as np
from nipype.utils.filemanip import fname_presuffix
Expand All @@ -519,7 +521,7 @@

bold_data = np.concatenate((bold_img.dataobj[..., :skip_vols], bold_cut_img.dataobj), axis=3)

out = fname_presuffix(bold_cut_file, suffix='_addnonsteady')
out = fname_presuffix(bold_cut_file, prefix='addnonsteady_', newpath=os.getcwd())

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bold_img.__class__(bold_data, bold_img.affine, bold_img.header).to_filename(out)
return out

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33 changes: 26 additions & 7 deletions src/fmripost_aroma/workflows/base.py
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Original file line number Diff line number Diff line change
Expand Up @@ -399,7 +399,26 @@
ica_aroma_wf.inputs.inputnode.confounds = functional_cache['confounds']
ica_aroma_wf.inputs.inputnode.skip_vols = skip_vols

if config.workflow.denoise_method and spaces.get_spaces():
if config.workflow.denoise_method:
# Now denoise the output-space BOLD data using ICA-AROMA
denoise_wf = init_denoise_wf(bold_file=bold_file)
denoise_wf.inputs.inputnode.skip_vols = skip_vols
denoise_wf.inputs.inputnode.space = 'MNI152NLin6Asym'
denoise_wf.inputs.inputnode.resolution = '2'

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workflow.connect([

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(mni6_buffer, denoise_wf, [
('bold_mni152nlin6asym', 'inputnode.bold_file'),
('bold_mask_mni152nlin6asym', 'inputnode.bold_mask'),
]),
(ica_aroma_wf, denoise_wf, [
('outputnode.mixing', 'inputnode.mixing'),
('outputnode.aroma_features', 'inputnode.classifications'),
]),
]) # fmt:skip

# Skip this for now
if config.workflow.denoise_method and spaces.get_spaces() and False:

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templates = spaces.get_spaces()
template_iterator_wf = init_template_iterator_wf(
spaces=spaces,
Expand All @@ -411,15 +430,15 @@
template_iterator_wf.inputs.inputnode.template = templates

# Now denoise the output-space BOLD data using ICA-AROMA
denoise_wf = init_denoise_wf(bold_file=bold_file)
denoise_wf.inputs.inputnode.skip_vols = skip_vols
denoise_std_wf = init_denoise_wf(bold_file=bold_file)
denoise_std_wf.inputs.inputnode.skip_vols = skip_vols

workflow.connect([
(ica_aroma_wf, denoise_wf, [
(ica_aroma_wf, denoise_std_wf, [
('outputnode.mixing', 'inputnode.mixing'),
('outputnode.aroma_features', 'inputnode.classifications'),
]),
(template_iterator_wf, denoise_wf, [
(template_iterator_wf, denoise_std_wf, [
('outputnode.space', 'inputnode.space'),
('outputnode.cohort', 'inputnode.cohort'),
('outputnode.resolution', 'inputnode.resolution'),
Expand All @@ -439,7 +458,7 @@
std_buffer.inputs.bold_mask = functional_cache['bold_mask_outputspaces']
workflow.connect([
(template_iterator_wf, std_buffer, [('outputnode.space', 'key')]),
(std_buffer, denoise_wf, [
(std_buffer, denoise_std_wf, [
('bold', 'inputnode.bold_file'),
('bold_mask', 'inputnode.bold_mask'),
]),
Expand Down Expand Up @@ -470,7 +489,7 @@
('outputnode.cohort', 'inputnode.cohort'),
]),
(all_xfms, resample_std_wf, [('out', 'inputnode.transforms')]),
(resample_std_wf, denoise_wf, [
(resample_std_wf, denoise_std_wf, [
('outputnode.bold_std', 'inputnode.bold'),
('outputnode.bold_mask_std', 'inputnode.bold_mask'),
]),
Expand Down